class: center, middle, inverse, title-slide # Data Science in the Time of Coronavirus ## Storytelling using the Data Science Platform ### Srikanth Aravamuthan ### University of Wisconsin-Madison ### January 17, 2024 --- <style> .center-mid { position: relative; top: 50%; transform: translateY(15%); } .kinda-center-mid { position: relative; top: 50%; transform: translateY(15%); } .center-left { position: relative; top: 50%; transform: translateY(30%); } .center-right { position: relative; top: 50%; transform: translateY(30%); } .big-text { font-size: 26px; padding: 0.5em 0em 0em 0em; line-height: 1.9em; } .kinda-big-text { font-size: 24px; padding: 0.2em 0em 0em 0em; } .kinda-small-text { font-size: 14px; } .really-big-text { font-size: 36px; } </style> # Background & Research .pull-left[ <!-- <img src="profile-picture.png" width="100%" border = "1"> --> <img src="profile-picture-1.jpg" width="100%"> ] .pull-right[ .kinda-big-text[ - Graduate Student in Comparative Biomedical Sciences - Background in Math & Science - Research in Computer Vision - Consulting Work in Statistics, Biostatistics, Computer Science - Contact: aravamuthan@wisc.edu ] ] --- # Overview .kinda-big-text[ - **COVID-19 Data Visualizations** - COVID-19 Growth Rates in Wisconsin - Geofaceting Instantaneous R<sub>0</sub> - COVID-19 Activity Level in Wisconsin - SARS-CoV-2 Screening Strategies - Nowcast COVID-19 Cases and Hospitalizations - **Automate DairyCOMP 305** - **Update DDCheck App** ] --- class: inverse, mline, center, middle # COVID-19 Data Visualizations of Descriptive Statistics Sean Kent, Steve Goldstein, and Brian Yandell (University of Wisconsin-Madison) Juan Francisco Mandujano Reyes & Dörte Döpfer (University of Wisconsin-Madison) --- # New York Times Data Visualizations .pull-left[ <center> <img src="data:image/png;base64,#nyt-upshot-headline.png" alt="diagonal layout" width="60%" border = "1"/> <img src="data:image/png;base64,#nyt-upshot-growth-rate-vs-time.png" alt="diagonal layout" width="60%" border = "1"/> </center> ] .pull-right[ <center> <img src="data:image/png;base64,#nyt-upshot-metro-box.png" alt="diagonal layout" width="60%" border = "1"/> <img src="data:image/png;base64,#nyt-upshot-growth-rate-vs-cases.png" alt="diagonal layout" width="60%" border = "1"/> </center> </br> <div style="width:300; word-wrap: break-word;"> <https://www.nytimes.com/interactive/2020/04/03/upshot/coronavirus-metro-area-tracker.html> </div> ] --- # COVID-19 Growth Rates in Wisconsin .kinda-big-text[ "*Wisconsin leaders need information about the extent and impact of COVID-19 to make good decisions.*" - **AFI DSI COVID-19 Research Group Charter** "*Can we add value with visualizations of growth rates in Wisconsin metro areas?*" - **Steve Goldstein** **Audience**: - Wisconsin public health officials - Health system officials - Interested modelers and citizens ] --- # COVID-19 Growth Rates in Wisconsin .pull-left[ <center> <img src="daily-growth-rate.png" height="200" border = "1"> </br> </br> <img src="map-metro-areas-cases.png" height="200" border = "1"> </center> ] .pull-right[ <center> <img src="growth-rate-case-count.png" height="200" border = "1"> </br> </br> <img src="map-metro-areas-deaths.png" height="200" border = "1"> </center> ] .center[ </br> [data-viz.it.wisc.edu/wi-metro-growth-rate/](https://data-viz.it.wisc.edu/wi-metro-growth-rate/) ] --- # COVID-19 Growth Rates in Wisconsin .pull-left[ <center> <img src="new-cases-case-count.png" width="100%" border = "1"> </center> ] .pull-right[ <center> <img src="new-cases-case-count-per-capita.png" width="100%" border = "1"> </center> ] --- # Publish Document or Website .pull-left[ .big-text[ - [data-viz.it.wisc.edu/wi-metro-growth-gundersen/](https://data-viz.it.wisc.edu/wi-metro-growth-gundersen/) - [data-viz.it.wisc.edu/wi-metro-growth-marshfield/](https://data-viz.it.wisc.edu/wi-metro-growth-marshfield/) ] ] .pull-right[ .big-text[ - Daily updates to new data - Customized to the needs of the heath system ] ] .center[ <img src="data:image/png;base64,#rstudio-server-pro.png" alt="diagonal layout" height="150"/> <img src="data:image/png;base64,#rstudio-connect.png" alt="diagonal layout" height="150"/> ] --- # Posit Connect Deployment .pull-left[ <img src="publishing-rmd.png" width="100%"> ] .pull-right[ .kinda-big-text[ - Standalone publishing platform - Dashboards - On-demand and scheduled reports - Interactive applications - User-friendly web application - Access controls - Performance settings - View logs ] ] --- # Geofaceting Instantaneous R<sub>0</sub> .kinda-big-text[ **Project Idea**: "*Can we summarize `\(R_0\)` spatially and temporally for all Wisconsin counties over all time points.*" **Audience**: - Wisconsin public health officials - Interested modelers ] --- # Geofaceting Instantaneous R<sub>0</sub> .pull-left[ <img src="instantaneous-r0.png" width="100%" border = "1"> ] .pull-right[ - Preserves the geographical orientation - Maintains the time dependence - Won honorable mention in John Hunter Excellence in Plotting Competition at SciPy 2020 - Website: [data-viz.it.wisc.edu/instantaneous-r0-geofacet-wi-county/](https://data-viz.it.wisc.edu/instantaneous-r0-geofacet-wi-county/) ] --- # COVID-19 Activity Level in Wisconsin .kinda-big-text[ **Project Idea**: - It would be helpful to overlay HERC regions on the county map - It would be helpful to view the census track level map - It would be helpful to see the time course **Audience**: - Wisconsin public health officials - Health system officials - Interested modelers and citizens ] --- # COVID-19 Activity Level in Wisconsin .pull-left[ <center> <img src="dhs-herc-regions.png" height="200" border = "1"> </br> </br> <img src="map-anim.png" height="200" border = "1"> </center> ] .pull-right[ <center> <img src="dhs-covid-19-activity-level.png" height="200" border = "1"> </br> </br> <img src="dane-county-map-anim.png" height="200" border = "1"> </center> ] .center[ </br> [data-viz.it.wisc.edu/dashboard/](https://data-viz.it.wisc.edu/dashboard/) ] --- # SARS-CoV-2 Screening Strategies .pull-left[ <center> <img src="data:image/png;base64,#paltiel-paper.png" width = "100%" border = "1"/> <img src="data:image/png;base64,#larremore-paper.png" width = "100%" border = "1"/> </center> </br> <div style="width:300; word-wrap: break-word;"> <https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2768923> </div> ] .pull-right[ <center> <img src="data:image/png;base64,#paltiel-model.png" alt="diagonal layout" width="100%"/> <img src="data:image/png;base64,#paltiel-iso-dorm.png" alt="diagonal layout" width="100%"/> </center> ] --- # SARS-CoV-2 Screening Strategies .kinda-big-text[ **Project Idea**: "*Can we implement an interactive dashboard with improved accessibility and ease of use.*" **Audience**: - University of Wisconsin-Madison campus leaders - Wisconsin public health officials - Health system officials - Interested modelers ] --- # SARS-CoV-2 Screening Strategies .pull-left[ <img src="paltiel-covid-19-dashboard.png" width="100%" border = "1"> ] .pull-right[ - Calculate minimum performance attributes of a SARS-CoV-2 monitoring program - Suggest what isolation and treatment capacity would need to be in place - Forecast what testing might cost - Recommended by the authors of the paper - Website: [data-viz.it.wisc.edu/covid-19-screening/](https://data-viz.it.wisc.edu/covid-19-screening/) ] --- # Nowcast COVID-19 Cases and Hospitalizations .kinda-big-text[ **Project Idea**: - Nowcast cases by HERC regions - Nowcast hospitalizations by HERC regions - View time series - View coverage of credible intervals ] .kinda-big-text[ **Audience**: - Wisconsin public health officials - Health system officials - Interested modelers ] --- # Nowcast COVID-19 Cases and Hospitalizations .pull-left[ <center> <img src="cases.png" height="200" border = "1"> </br> </br> <img src="hosp.png" height="200" border = "1"> </center> ] .pull-right[ <center> <img src="r.png" height="200" border = "1"> </br> </br> <img src="coverage-all-reference.png" height="200" border = "1"> </center> ] .center[ </br> [https://data-viz.it.wisc.edu/cases-r-hosp-geofacet-wi-region/](https://data-viz.it.wisc.edu/cases-r-hosp-geofacet-wi-region/) ] --- # Publish Datasets .pull-left[ <img src="pins-1.png" width="100%"> ] .pull-right[ .kinda-big-text[ - Daily updates to new data - Customized to the needs of the public heath system - Publishes data, models, and other R objects - Easy to share across projects and with users - Automatically versioned - Track changes, re-run analyses on historical data, and undo mistakes ] ] --- layout: false class: inverse, center, middle # **Cow Break!** <center> <img src="happy-cow.jpg" width="50%" border = "1"> </center> --- class: inverse, mline, center, middle # Automate DairyCOMP 305 Emil Walleser & Dörte Döpfer (University of Wisconsin-Madison) --- # DairyCOMP 305 .pull-left[ <img src="dairy-comp.png" width="100%" border = "1"> ] .pull-right[ <img src="dairy-comp-1.png" width="100%" border = "1"> ] --- # Motivation .pull-left[ <img src="ketosis-analysis.png" width="100%" border = "1"> ] .pull-right[ .kinda-big-text[ - Health data is locked in DairyCOMP 305 - Limited integrated analysis - Extensive preprocessing ] ] --- # DairyCOMP 305 .center-mid[ .center[ <img src="no.gif" height="100%" border = "1"> ] ] --- # Automate DairyCOMP 305 .kinda-big-text[ **Project Idea**: - Automate DairyCOMP 305 write out - Apply tools to support data-driven decisions - Customize reports and graphs for a better management experience ] .kinda-big-text[ **Audience**: - DairyCOMP 305 users - Dairy Skills I instructors & students ] --- # Dairy Co-Pilot .pull-left[ <img src="dairy-copilot.png" width="100%"> ] .pull-right[ .kinda-big-text[ - Simplify data wrangling in DairyCOMP 305 - Reduce time for data cleaning - Simplify analysis - Enhance analysis - Website: [connect.doit.wisc.edu/dairy-copilot/](https://connect.doit.wisc.edu/dairy-copilot/) ] ] --- class: inverse, mline, center, middle # Update DDCheck App Dörte Döpfer (University of Wisconsin-Madison) --- # DDCheck App .center-mid[ .center[ <img src="dd-check.jpg" height="100%" border = "1"> ] ] --- # Update DDCheck App .kinda-big-text[ **Project Idea**: - Update DDCheck user interface - Apply computer vision tools to support data-driven decisions - Customize reports and graphs for a better management experience ] .kinda-big-text[ **Audience**: - Veterinarians, hoof trimmers, farmers, and herd managers - Instructors and students ] --- # DDCheckPlus App .pull-left[ <img src="dd-check-plus.png" width="100%"> ] .pull-right[ .kinda-big-text[ - Simplify data recording - Reduce time for data analysis - Simplify analysis - Enhance analysis - Website: [connect.doit.wisc.edu/dd-check/](https://connect.doit.wisc.edu/dd-check/) ] ] --- # DD Detection Module .pull-left[ <center> <img src="dd-detection-module.jpg" height="50%" border = "1"> </center> ] .pull-right[ .kinda-big-text[ - Computer vision aided data recording - YOLOv5s Core ML model on iOS/iPadOS device - Fast with sufficient accuracy ] ] --- # R Shiny App .pull-left[ <img src="r-shiny-app.png" width="100%" border = "1"> ] .pull-right[ .kinda-big-text[ - Machine learning assisted data analysis - Predict prevalence of disease in its various stages - User-friendly web application ] ] --- # Update DDCheck App .center-mid[ .center[ <img src="welcome.gif" height="100%" border = "1"> ] ] --- # Presentation Application .center-mid[ .center[ <img src="xaringan.png" height="400" border = "1"> ] ] --- layout: false class: inverse, center, middle # **Thank You!** <center> <img src="meeting.gif" width="25%" border = "1"> </br> </br> <div style="width:300; font-weight:bold; word-wrap: break-word;"> Contact: <a href = "mailto: aravamuthan@wisc.edu">aravamuthan@wisc.edu</a> </br> Website: <a href = "https://connect.doit.wisc.edu/posit-day/">connect.doit.wisc.edu/posit-day/</a> </div> </center>